Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'15-Hairpin pdb2qbk1B.e2599-2615
Source: [PDB-id:chain] 2qbk:B (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH GENTAMICIN AND RIBOSOME RECYCLING FACTOR (RRF). THIS FILE CONTAINS THE 50S SUBUNIT OF THE SECOND 70S RIBOSOME, WITH GENTAMICIN AND RRF BOUND. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND IS DESCRIBED IN REMARK 400.
Source: Compound 23S RRNA
Source: Resolution 4.00 ANGSTROMS.
Position (2599, 2615)
Primary structure ('_': anchors) _UAGUACGAGAGGACC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		15: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 &larr
3 3 5 →
4 4 13 &larr
5 6 7 ↑
6 6 14 →
7 7 8 ↑
8 9 10 ↑
9 10 11 ↑
10 11 12 ↑
11 12 13 ↑
12 14 15 &larr
13 15 16 →
14 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 17 Watson-Crick/Watson-Crick cis
2 2 16 Watson-Crick/Watson-Crick cis y
3 3 15 O2'/Bifurcated trans
4 4 5 Hoogsteen/Sugar cis y
5 4 14 O2'/Bifurcated ?
6 5 13 Bifurcated/O2' ?
7 5 14 Hoogsteen/Watson-Crick trans
8 6 13 O2'/Bifurcated trans
9 7 12 Watson-Crick/Watson-Crick cis
10 8 10 O2'/Sugar ?
11 8 11 O2'/Bifurcated ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters